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Description

Title :   CRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS 10 AND 11

Authors :   S. D. Chatziefthimiou, N. Pinotsis, M. Wilmanns

Date :   29 Mar 11 (Deposition) - 07 Mar 12 (Release) - 07 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Immunoglobulin C-Set Domain, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Pinotsis, S. D. Chatziefthimiou, F. Berkemeier, F. Beuron, I. M. Mavridis, P. V. Konarev, D. I. Svergun, E. Morris, M. Rief, M. Wilmanns
Superhelical Architecture Of The Myosin Filament-Linking Protein Myomesin With Unusual Elastic Properties.
Plos Biol. V. 10 01261 2012
PubMed-ID: 22347812 | Reference-DOI: 10.1371/JOURNAL.PBIO.1001261

Compounds

Molecule 1 - MYOMESIN-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3) CODON PLUS-RP
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET151/D-TOPO
	Fragment	:	MYOMESIN-1 DOMAINS 10 AND 11, UNP RESIDUES 1247-1447
	Gene	:	MYOM1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	190 KDA CONNECTIN-ASSOCIATED PROTEIN, 190 KDA TITIN- ASSOCIATED PROTEIN, MYOMESIN FAMILY MEMBER 1

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 5)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	BME	3	Ligand/Ion	BETA-MERCAPTOETHANOL
2	NO3	2	Ligand/Ion	NITRATE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:157 , TYR A:1363 , LEU A:1364 , SER A:1439 , ARG A:1440	BINDING SITE FOR RESIDUE BME A 1
2	AC2	SOFTWARE	CYS A:1372 , GLU A:1417	BINDING SITE FOR RESIDUE BME A 2
3	AC3	SOFTWARE	HOH A:99 , HOH A:117 , HOH A:129 , HOH A:131 , HOH A:132 , GLU A:1397 , SER A:1399 , VAL A:1400	BINDING SITE FOR RESIDUE BME A 3
4	AC4	SOFTWARE	HOH A:170 , TYR A:1392 , GLU A:1427	BINDING SITE FOR RESIDUE NO3 A 1448
5	AC5	SOFTWARE	HOH A:116 , GLY A:1271 , ASN A:1272 , ALA A:1273 , ARG A:1296	BINDING SITE FOR RESIDUE NO3 A 1449

SS Bonds (0, 0)

(no "SS Bond" information available for 3RBS)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3RBS)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047227	D	1408	N	MYOM1_HUMAN	Polymorphism	3765623	A	D	1408	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 3RBS)

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000356443	1	ENSE00001400333	chr18:3220106-3219801	306	MYOM1_HUMAN	-	0	0	-	-
1.2	ENST00000356443	2	ENSE00001543713	chr18:3215249-3214932	318	MYOM1_HUMAN	1-97	97	0	-	-
1.3	ENST00000356443	3	ENSE00001403202	chr18:3193956-3193816	141	MYOM1_HUMAN	97-144	48	0	-	-
1.4	ENST00000356443	4	ENSE00001240625	chr18:3189085-3188746	340	MYOM1_HUMAN	144-257	114	0	-	-
1.5	ENST00000356443	5	ENSE00001240622	chr18:3187635-3187478	158	MYOM1_HUMAN	258-310	53	0	-	-
1.6	ENST00000356443	6	ENSE00001240619	chr18:3176132-3176040	93	MYOM1_HUMAN	310-341	32	0	-	-
1.7	ENST00000356443	7	ENSE00001240615	chr18:3174206-3174118	89	MYOM1_HUMAN	341-371	31	0	-	-
1.8	ENST00000356443	8	ENSE00001240608	chr18:3173998-3173936	63	MYOM1_HUMAN	371-392	22	0	-	-
1.9	ENST00000356443	9	ENSE00001240603	chr18:3168979-3168815	165	MYOM1_HUMAN	392-447	56	0	-	-
1.10	ENST00000356443	10	ENSE00001240598	chr18:3164437-3164276	162	MYOM1_HUMAN	447-501	55	0	-	-
1.11	ENST00000356443	11	ENSE00001240595	chr18:3155086-3154945	142	MYOM1_HUMAN	501-548	48	0	-	-
1.12	ENST00000356443	12	ENSE00001240590	chr18:3151891-3151692	200	MYOM1_HUMAN	548-615	68	0	-	-
1.13	ENST00000356443	13	ENSE00001240585	chr18:3149199-3149143	57	MYOM1_HUMAN	615-634	20	0	-	-
1.14	ENST00000356443	14	ENSE00001240581	chr18:3142061-3141937	125	MYOM1_HUMAN	634-675	42	0	-	-
1.15	ENST00000356443	15	ENSE00001240577	chr18:3135728-3135545	184	MYOM1_HUMAN	676-737	62	0	-	-
1.16	ENST00000356443	16	ENSE00001240573	chr18:3134822-3134648	175	MYOM1_HUMAN	737-795	59	0	-	-
1.17	ENST00000356443	17	ENSE00001240567	chr18:3131494-3131373	122	MYOM1_HUMAN	795-836	42	0	-	-
1.18	ENST00000356443	18	ENSE00001413714	chr18:3129517-3129230	288	MYOM1_HUMAN	836-932	97	0	-	-
1.19	ENST00000356443	19	ENSE00001240558	chr18:3126895-3126699	197	MYOM1_HUMAN	932-997	66	0	-	-
1.20	ENST00000356443	20	ENSE00001240553	chr18:3119993-3119867	127	MYOM1_HUMAN	998-1040	43	0	-	-
1.21	ENST00000356443	21	ENSE00001240549	chr18:3116513-3116329	185	MYOM1_HUMAN	1040-1101	62	0	-	-
1.22	ENST00000356443	22	ENSE00001240541	chr18:3112410-3112296	115	MYOM1_HUMAN	1102-1140	39	0	-	-
1.23	ENST00000356443	23	ENSE00001240535	chr18:3102628-3102472	157	MYOM1_HUMAN	1140-1192	53	0	-	-
1.24	ENST00000356443	24	ENSE00001240526	chr18:3100424-3100318	107	MYOM1_HUMAN	1192-1228	37	0	-	-
1.25	ENST00000356443	25	ENSE00001240522	chr18:3100201-3100157	45	MYOM1_HUMAN	1228-1243	16	0	-	-
1.26b	ENST00000356443	26b	ENSE00001240516	chr18:3094304-3094168	137	MYOM1_HUMAN	1243-1288	46	1	A:1246-1288	43
1.27	ENST00000356443	27	ENSE00001592917	chr18:3090800-3090656	145	MYOM1_HUMAN	1289-1337	49	1	A:1289-1337	49
1.28	ENST00000356443	28	ENSE00001709505	chr18:3089594-3089535	60	MYOM1_HUMAN	1337-1357	21	1	A:1337-1357	21
1.29	ENST00000356443	29	ENSE00001645638	chr18:3089239-3089172	68	MYOM1_HUMAN	1357-1379	23	1	A:1357-1379	23
1.30	ENST00000356443	30	ENSE00001692605	chr18:3086149-3086036	114	MYOM1_HUMAN	1380-1417	38	1	A:1380-1417	38
1.31	ENST00000356443	31	ENSE00001738311	chr18:3085130-3085043	88	MYOM1_HUMAN	1418-1447	30	1	A:1418-1446	29
1.32	ENST00000356443	32	ENSE00001676386	chr18:3084025-3083987	39	MYOM1_HUMAN	1447-1460	14	0	-	-
1.33	ENST00000356443	33	ENSE00001782333	chr18:3083892-3083787	106	MYOM1_HUMAN	1460-1495	36	0	-	-
1.34	ENST00000356443	34	ENSE00001735824	chr18:3079340-3079177	164	MYOM1_HUMAN	1495-1550	56	0	-	-
1.35	ENST00000356443	35	ENSE00001803821	chr18:3075759-3075723	37	MYOM1_HUMAN	1550-1562	13	0	-	-
1.36	ENST00000356443	36	ENSE00001731412	chr18:3075474-3075452	23	MYOM1_HUMAN	1562-1570	9	0	-	-
1.37	ENST00000356443	37	ENSE00001618984	chr18:3071887-3071832	56	MYOM1_HUMAN	1570-1588	19	0	-	-
1.38	ENST00000356443	38	ENSE00001615622	chr18:3067553-3066805	749	MYOM1_HUMAN	1589-1685	97	0	-	-

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:201
 aligned with MYOM1_HUMAN | P52179 from UniProtKB/Swiss-Prot  Length:1685

    Alignment length:201
                                  1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445 
         MYOM1_HUMAN   1246 VKSELAVEILEKGQVRFWMQAEKLSGNAKVNYIFNEKEIFEGPKYKMHIDRNTGIIEMFMEKLQDEDEGTYTFQLQDGKATNHSTVVLVGDVFKKLQKEAEFQRQEWIRKQGPHFVEYLSWEVTGECNVLLKCKVANIKKETHIVWYKDEREISVDEKHDFKDGICTLLITEFSKKDAGIYEVILKDDRGKDKSRLKLVDE 1446
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhh.eeeeee........eeeeee..eee......eeee.....eeeeee...hhhhheeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeee......eeeeee..eee..........eeeeeee...hhhhheeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.26b  PDB: A:1246-1288 [INCOMPLETE]  Exon 1.27  PDB: A:1289-1337 UniProt: 1289-1337   -------------------Exon 1.29              Exon 1.30  PDB: A:1380-1417           Exon 1.31  PDB: A:1418-1446   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------Exon 1.28            ----------------------------------------------------------------------------------------- Transcript 1 (2)
                3rbs A 1246 TKSELAVEILEKGQVRFWMQAEKLSGNAKVNYIFNEKEIFEGPKYKMHIDRNTGIIEMFMEKLQDEDEGTYTFQLQDGKATNHSTVVLVGDVFKKLQKEAEFQRQEWIRKQGPHFVEYLSWEVTGECNVLLKCKVANIKKETHIVWYKDEREISVDEKHDFKDGICTLLITEFSKKDAGIYEVILKDDRGKDKSRLKLVDE 1446
                                  1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 3RBS)

CATH Domains (0, 0)

(no "CATH Domain" information available for 3RBS)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3RBS)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MYOM1_HUMAN | P52179)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008307	structural constituent of muscle	The action of a molecule that contributes to the structural integrity of a muscle fiber.
biological process
	GO:0006936	muscle contraction	A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
	GO:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
	GO:0031430	M band	The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0032982	myosin filament	A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0005863	striated muscle myosin thick filament	Bipolar filaments formed of polymers of a muscle-specific myosin II isoform, found in the middle of sarcomeres in myofibrils.

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	MYOM1_HUMAN \| P52179	:	2r15 2y23 2y25 5fm4 5fm5 5fm8

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